The Gunners conceded two quick goals to Gareth Bale and Aaron Lennon before half-time after keeping Spurs quiet before dominating the second half but only scoring once via Per Mertesacker's deflected header.
The loss enlarged Spurs' gap to seven points on their North London rivals and Wenger found the result hard to accept.
"It is difficult to swallow a defeat like that because of the effort we put in," he told Sky Sports.
"We made it difficult for ourselves. They had no shots on goal and then we were down 2-0.
"We came back in the second half and dominated the game again, but it was difficult to get a flow in the final 20 minutes because there were a lot of stops and we didn't find a second goal."